--- a
+++ b/man/run_cicero_wrapper.Rd
@@ -0,0 +1,56 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/method_wrappers.R
+\name{run_cicero_wrapper}
+\alias{run_cicero_wrapper}
+\title{Cicero wrapper function for the compute_atac_peak_network function}
+\usage{
+run_cicero_wrapper(
+  hummus,
+  atac_assay,
+  genome,
+  window,
+  number_cells_per_clusters,
+  sample_num,
+  seed,
+  verbose,
+  threshold,
+  reduction_method = "UMAP"
+)
+}
+\arguments{
+\item{hummus}{A hummus object}
+
+\item{atac_assay}{The name of the assay containing the scATAC-seq data}
+
+\item{genome}{The genome object}
+
+\item{window}{The window size used by Cicero to compute the coaccess score}
+
+\item{number_cells_per_clusters}{The number of cells per cluster used by
+Cicero to compute the coaccess score}
+
+\item{sample_num}{The number of samples used by Cicero to compute the
+coaccess score}
+
+\item{seed}{The seed used by Cicero to compute the coaccess score}
+
+\item{verbose}{The verbosity level}
+
+\item{threshold}{The threshold used to filter edges based on the coaccess
+score}
+
+\item{reduction_method}{The method used by monocle3 to reduce the dimension
+of the scATAC-seq data before defining the pseudocells. The default is UMAP.}
+}
+\value{
+A data frame containing the peak network
+}
+\description{
+This function is a wrapper for the compute_atac_peak_network
+function in layers.R. It computes the peak network from scATAC-seq data
+using Cicero. It returns a data frame with the peak network. The data frame
+also contains the coaccess score for each edge. The coaccess score is the
+probability that two peaks are accessible in the same cell. The coaccess
+score is computed by Cicero. Edges are filtered based on the coaccess score.
+Only edges with a coaccess score > threshold are kept.
+}